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Open data
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Basic information
Entry | Database: PDB / ID: 3rcz | ||||||
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Title | Rad60 SLD2 Ubc9 Complex | ||||||
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![]() | protein binding/Ligase / SUMO-like Domain / protein:protein interaction / Ubc9 / protein binding-Ligase complex | ||||||
Function / homology | ![]() regulation of mitotic chromosome condensation / SUMO E3 ligases SUMOylate target proteins / : / SUMO ligase regulator activity / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of DNA replication proteins / SUMOylation of DNA damage response and repair proteins / SUMOylation of nuclear envelope proteins ...regulation of mitotic chromosome condensation / SUMO E3 ligases SUMOylate target proteins / : / SUMO ligase regulator activity / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of DNA replication proteins / SUMOylation of DNA damage response and repair proteins / SUMOylation of nuclear envelope proteins / heterochromatin => GO:0000792 / SUMOylation of transcription factors / SUMOylation of transcription cofactors / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / Postmitotic nuclear pore complex (NPC) reformation / SUMO activating enzyme activity / SUMOylation of chromatin organization proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / SUMO conjugating enzyme activity / Transferases; Acyltransferases; Aminoacyltransferases / replication fork processing / protein sumoylation / double-strand break repair via homologous recombination / DNA repair / ATP binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Perry, J.J.P. / Arvai, A.S. / Tainer, J.A. | ||||||
![]() | ![]() Title: DNA repair and global sumoylation are regulated by distinct Ubc9 noncovalent complexes. Authors: Prudden, J. / Perry, J.J. / Nie, M. / Vashisht, A.A. / Arvai, A.S. / Hitomi, C. / Guenther, G. / Wohlschlegel, J.A. / Tainer, J.A. / Boddy, M.N. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 63.6 KB | Display | ![]() |
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PDB format | ![]() | 46.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433 KB | Display | ![]() |
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Full document | ![]() | 435.4 KB | Display | |
Data in XML | ![]() | 12.7 KB | Display | |
Data in CIF | ![]() | 18 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3rd2C ![]() 3goeS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 9793.047 Da / Num. of mol.: 1 / Fragment: SUMO-like Domain 2, UNP residues 332-406 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: rad60, SPBC1921.02 / Production host: ![]() ![]() |
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#2: Protein | Mass: 18843.615 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: hus5, ubc9, SPAC30D11.13 / Production host: ![]() ![]() References: UniProt: P40984, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.8 Details: 20% PEG 8K, 200 mM imidazole malate buffer, pH 5.8, 600 mM LiNO3 and 1 mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 5, 2009 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 21180 / Num. obs: 20990 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 30 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3GOE.pdb Resolution: 1.9→33.265 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0.08 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.732 Å2 / ksol: 0.362 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.9→33.265 Å
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Refine LS restraints |
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LS refinement shell |
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